Well-ordered cubic FDU-12 type mesoporous silicas functionalized with various contents of carboxylic acid group (COOH), up to 40mol% based on silica, were synthesized via co-condensation of tetraethyl orthosilicate (TEOS) and carboxyethylsilanetriol sodium salt (CES) under acidic conditions using Pluronic F127 triblock copolymer as template. The materials thus obtained were characterized by a variety of techniques including powder X-ray diffraction (XRD), nitrogen adsorption-desorption, transmission electron microscopy (TEM), 13C and 29Si solid-state nuclear magnetic resonance (NMR) measurements. The materials were used as adsorbents for removal of methylene blue (MB) in aqueous solutions and as an antidote for intoxication of herbicide paraquat (PQ). Due to the COOH functionalization, three-dimensional pores, high surface areas, and electrostatic interactions between the adsorbent and the adsorbates, the prepared adsorbents possessed very high adsorption capacities and extremely rapid rates for MB and PQ adsorption. The kinetic regression results revealed that the overall adsorption process was controlled by external mass transfer and intra-particle diffusion jointly. The Langmuir isotherm model showed better fit with the experimental adsorption data than the Freundlich isotherm model, implying a monolayer adsorption mechanism. The present results show that the prepared COOH functionalized cubic mesoporous silicas have great potentials for removing pollutants and herbicides from aqueous solutions in environmental and clinical applications.